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This page was generated on 2021-10-15 15:05:55 -0400 (Fri, 15 Oct 2021).

CHECK results for trio on nebbiolo1

To the developers/maintainers of the trio package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/trio.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1963/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trio 3.30.0  (landing page)
Holger Schwender
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/trio
git_branch: RELEASE_3_13
git_last_commit: 0ed315f
git_last_commit_date: 2021-05-19 12:00:07 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: trio
Version: 3.30.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:trio.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings trio_3.30.0.tar.gz
StartedAt: 2021-10-14 11:56:17 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:58:47 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 149.8 seconds
RetCode: 0
Status:   OK  
CheckDir: trio.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:trio.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings trio_3.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/trio.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘trio/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trio’ version ‘3.30.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘trio’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .C("clogreg", ..., PACKAGE = "LogicReg")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
print.trioFS 8.333  0.248  13.018
colGxGPerms  5.105  0.024   5.130
trioFS       4.705  0.357   5.063
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/trio.Rcheck/00check.log’
for details.



Installation output

trio.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL trio
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘trio’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘trio.Rnw’ 
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (trio)

Tests output


Example timings

trio.Rcheck/trio-Ex.timings

nameusersystemelapsed
allelicTDT0.0280.0000.027
colEMlrt0.1110.0040.115
colGxE0.0090.0000.010
colGxGPerms5.1050.0245.130
colPOlrt0.0160.0000.017
colTDTmaxTest0.0450.0000.044
colTDTsam0.0380.0000.038
findLDblocks0.0220.0000.022
getLD0.0160.0000.015
getMatPseudo0.0140.0000.014
lrControl0.0010.0000.000
ped2geno0.0010.0000.000
plot.LDblocks0.0470.0000.047
plot.getLD0.030.000.03
plot.trioLR3.5140.0723.593
poly4root0.0010.0000.001
print.colGxE0.4390.0160.454
print.trioFS 8.333 0.24813.018
print.trioLR3.3440.0403.719
probTDT0.0680.0240.092
read.pedfile0.0010.0000.001
removeSNPs0.0080.0000.008
scoreTDT0.0120.0000.012
tdt0.0220.0080.030
tdtGxG2.2030.0162.308
trio.check0.5870.0000.587
trio.data0.0060.0000.006
trio.permTest4.1730.1044.277
trio.power0.0120.0000.012
trio.prepare2.0180.0082.028
trio.sim0.4000.0010.401
trioFS4.7050.3575.063
trioLR2.0850.0962.182